grep pattern in both start and end, but with mismatch in the middle of sequence

Question

[l.willianpacheco]

Hi everyone

I'm looking for a method to perform grep in both start and end of a sequencing, but allowing one, two or three mismatch in the middle.

[conservative match] + match with maximum of three mismatch + [conservative match]

I tried grep from seqkit, but this tool allow mismatch in the entire sequence.

Best regards, Willian

[GenoMax]

This may be what you are looking for: https://unix.stackexchange.com/questions/163726/limit-grep-context-to-n-characters-on-line

If these are fastq files then some creative combination of restrictright= and restrictleft= may work with bbduk.sh in filter mode. A guide is available here: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/